Method for treating inflammatory bowel disease and other forms of gastrointestinal inflammation

ABSTRACT

The invention provides a method for ameliorating gastrointestinal inflammation, particularly chronic gastrointestinal inflammation such as inflammatory bowel disease (IBD), in a subject. In one embodiment, the method comprises administering an immunomodulatory nucleic acid to a subject suffering from or susceptible to gastrointestinal inflammation.

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit of U.S. ProvisionalApplication Serial No. 60/184,256, filed Feb. 23, 2000, whichapplication is incorporated herein by reference in its entirety.

STATEMENT AS TO FEDERALLY SPONSORED RESEARCH

[0002] This invention was made with Government support under Grant No.AI40682, awarded by the National Institutes of Health. The governmenthas certain rights in this invention.

[0003] Throughout this application various publications are referenced.The disclosures of these publications in their entireties are herebyincorporated by reference into this application in order to describemore fully the state of the art to which this invention pertains.

TECHNICAL FIELD OF THE INVENTION

[0004] The invention relates to a method for ameliorating inflammationof the gastrointestinal tract, such as that associated with inflammatorybowel disease, in a subject. The method involves administering a nucleicacid comprising an immunomodulatory nucleotide sequence to the subject.The immunomodulatory sequence can be administered alone or together withan additional therapeutic agents.

BACKGROUND OF THE INVENTION

[0005] Gastrointestinal inflammation is one of the most common types ofinflammatory process which affects humans (for a review, see, e.g.,Bamford, FEMS Immunol Med Microbiol (1999) 24(2):161-8). Inflammatorybowel disease (IBD), a form of chronic gastrointestinal inflammation,includes a group of chronic inflammatory disorders of generally unknownetiology, e.g., ulcerative colitis (UC) and Crohn's disease (CD).Clinical and experimental evidence suggest that the pathogenesis of IBDis multifactorial involving susceptibility genes and environmentalfactors (Sartor Am J Gastroenterol. (1997) 92:5S-11S). The interactionof these factors with the immune system leads to intestinal inflammationand dysregulated mucosal immunity against commensal bacteria, variousmicrobial products (e.g., LPS) or antigens (Mayer et al. Current conceptof IBD: Etiology and pathogenesis. In “Inflammatory Bowel Disease”5^(th) edition 2000, Kirsner JB editor. W. B. Sanunders Company, pp280-296; for a discussion of IBD in children see, e.g., Walker-Smith,Postgrad Med J (2000) 76(898):469-72).

[0006] Human Crohn3 s disease (CD) is thought to be characterized bytype 1 Helper T (Th-1) response, which produce the cytokines interleukinIL-2, interferon γ, and tumor necrosis factor TNF (for a review ofanti-TNFα therapy in Crohn's disease, see, e.g., Mikula GastroenterolNurs. (1999) 22(6):245-8; Selby, Vet Microbiol (2000) 77(3-4): 505-511). Ulcerative colitis (UC) is dominated by type 2 Helper T (Th-2)response which produce anti-inflammatory cytokines such as IL-4, IL-5and IL-10. However, the demarcation between Th-1 and Th-2 response in CDand UC is not an “all or none” response and it seems that there issignificant overlap.

[0007] Animal models of colitis have highlighted the prominent role ofCD4+T cells in the regulation of intestinal inflammation (Blumberg etal. Curr Opin Immunol (1999) 6:648-56). Cytokine imbalance, and theproduction of inflammatory mediators have been postulated to play animportant role in the pathogenesis of both experimental colitis and IBD(Papadakis et al. Annu Rev Med (2000) 51:289-98; for a review, see,e.g., Blumberg JAMA (2001) 285(5):643-647; Nagura et al. Digestion(2001) 63 Suppl Si:12-21). In particular, dysregulated CD4+T cellresponses play a pivotal role in the pathogenesis of experimentalcolitis (Bhan et al. Immunol Rev (1999) 169:195-207). Indeed, Thlcytokines (e.g., IL-12) are dominant in inflamed mucosa of CD, whereasTh2 cytokines (e.g., IL-4) are relatively common in UC. In this respect,dinitrobenzene sulphonic acid-induced colitis (DNB), which ischaracterized by predominating Th1 response in mice (Neurath et al. IntRev Immunol (2000) 19:51-6) mimics CD, whereas dextran sodium sulphate(DSS) induces acute and chronic colitis with a mixed Th1/Th2-likeresponse, features UC (Dieleman et al. Clin Exp Immunol (1998)114:385-91). Studies using transgenic mice having deletions in acytokine gene develop a spontaneous inflammatory bowel disease (for areview see, e.g., MacDonald, Eur J Gastroenterol Hepatol (1997)9(11):1051-50). animals having cytokine DNB-induced colitis, which isdriven by mucosal Th1 response, has been reported to be accelerated byrIL-12 and inhibited by administration of anti-IL-12 antibodies (Neurtahet al. (2000), ibid). The inflammatory process and the immune responseat mucosal sites result in mucosal barrier dysfunction leading tofurther exposure to enteric bacteria and/or their products thatperpetuate mucosal inflammation (Podolsky Am J Physiol (1999)277:G495-9).

[0008] Immunosuppressive and anti-inflammatory agents in highmaintenance doses are the principal drugs used in the therapy of chronicinflammatory gastrointestinal disorders. Anti-inflammatory drugspresently used in treatment of IBD include aminosalycilates andimmunosuppressive agents such as corticosteroids, azathioprine,cyclosporine and methotrexate. Corticosteroids remain the mainstay ofanti-inflammatory and immunosuppressive therapy for manygastrointestinal conditions (see, e.g., Hyams, Curr Opin Pediatr (2000);12(5):451-5). Recently, specific anti-TNF antibodies have been used fortreatment of IBD. About 20-25% of the patients with UC fail to respondto intensive and optimal medical therapy and therefore are referred tosurgery for total proctocolectomy. In general, patients with CD are lessresponsive to medical therapy and usually do not respond to surgicaltreatment. Recently, anti-TNFα antibodies were introduced to treatpatients with CD with reasonable efficacy, but this approach isineffective in patients with UC. Thus, IBD is a medical problem thatlacks an effective treatment.

[0009] The importance of management of gastrointestinal inflammation,particular chronic gastrointestinal inflammation, can not beunderestimated, since the presence of gastrointestinal inflammation canbe an early sign for risk of development of further serious conditions.For example, colorectal cancer represents the major cause for excessmorbidity and mortality by malignant disease in ulcerative colitis aswell as in Crohn's disease. The risk for ulcerative colitis associatedcolorectal cancer is increased at least 2-fold compared to the normalpopulation. Colorectal cancer is observed in 5.5-13.5% of all patientswith ulcerative colitis and 0.4-0.8% of patients with Crohn's disease.Ulcerative colitis associated colorectal cancer typically can occur inthe entire colon, is often multifocal and of undifferentiated histology.Stage distribution and prognosis of ulcerative colitis associatedcolorectal cancer appears to be similar to that of sporadic colorectalcancer with an overall survival of about 40% (15-65%) after 5 years withtumor stage at diagnosis being the most important predictive parameterfor survival (for a review see, e.g., Pohl et al. Hepatogastroenterology(2000) 47(31):57-70).

[0010] There is a need in the field for effective methods of treatinggastrointestinal inflammation, particularly chronic gastrointestinalinflammation such as IBD. The present invention addresses this need.

SUMMARY OF THE INVENTION

[0011] The invention provides a method for ameliorating gastrointestinalinflammation, particularly chronic gastrointestinal inflammation such asinflammatory bowel disease (IBD), in a subject. In one embodiment, themethod comprises administering an immunomodulatory nucleic acid to asubject suffering from or susceptible to gastrointestinal inflammation.

[0012] The immunomodulatory nucleic acid can be administered viagastroenteral or parenteral routes. Examples of gastroenteral routesinclude, but are not limited to, oral, gastric or rectal administration.Examples of parenteral routes include, but are not limited to,intradermal, intramuscular, subcutaneous or intravenous administration.The immunomodulatory nucleic acid can be administered alone or togetherwith additional therapeutic agents.

[0013] In exemplary embodiments, the immunomodulatory nucleic acidcomprises a non-coding oligonucleotide sequence that may include atleast one unmethylated CpG motif. Examples of an immunomodulatorynucleic acid include, but are not limited to, sequences comprising5′-rrcgyy-3′, such as AACGTT, AGCGTT, GACGTT, GGCGTT, AACGTC, andAGCGTC, 5′-rycgyy-3′ such as GTCGTT, 5′-rrcgyycg-3′, 5′-rycgyycg-3′ or5′-(TCG)_(n)-3′. An immunomodulatory nucleic acid of particular interestis one comprising the sequence 5′-AACGTTCG-3′. In one exemplaryembodiment, the immunomodulatory nucleic acid is plasmid DNA orbacterial genomic DNA.

BRIEF DESCRIPTION OF THE FIGS.

[0014] FIGS 1A-1D are graphs showing the effects of a singlesubcutaneous administration of immunomodulatory polynucleotide orcontrol M-ODN (10 μg/mouse), administered 2 hrs prior to DSS challenge,in an animal model of colitis. Disease activity index (DAI) (FIG. 1A),change in body weight (FIG. 1B) colonic weight (FIG. 1C) and colonic MPOactivity (FIG. 1D) were reduced in immunomodulatorypolynucleotide-treated animals. Data represent one experiment out ofthree.

[0015]FIG. 2 is a graph showing the effect of various immunomodulatorypolynucleotide upon disease activity index in DSS-induced colitis.

[0016] FIGS. 3A-3C are graphs showing the dose-response effect ofsubcutaneous immunomodulatory polynucleotide administration upon bodyweight (FIG. 3A), disease activity index (FIG. 3B), and colonic weight(FIG. 3C) in a DSS-induced animal model of colitis.

[0017]FIG. 4 is a bar graph showing the effect of immunomodulatorypolynucleotide upon disease activity index in a DSS-induced animal modelof colitis when administered subcutaneously 48 hours after DSS exposure(e.g., in a therapeutic mode).

[0018]FIG. 5 is a graph showing the effects of administration ofintragastric immunomodulatory polynucleotide two hours prior toinduction of colitis by administration of DSS in an animal model.

[0019] FIGS. 6A-6C are graphs showing the dose-response effect ofintragastric immunomodulatory polynucleotide administration upon bodyweight (FIG. 6A), disease activity index (FIG. 6B), and colonic weight(FIG. 6C) in a DSS-induced animal model of colitis.

[0020] FIGS. 7A-7F are exemplary results from RT-PCR and Western blotanalysis of colonic tissues of naive (no DSS, no polynucleotide),DSS-treated (DSS), DSS and control M-ODN treated (DSS+M-ODN), andDSS-treated, immunomodulatory polynucleotide-treated (DSS+ISS) mice.

[0021] FIGS. 8A-8E are photographs of H&E stained sections of colontaken from control, DSS-treated, or DSS-treated and immunomodulatorypolynucleotide-treated mice. FIG. 8A, control (no DSS, nopolynucleotide); FIG. 8B, DSS alone; FIG. 8C, DSS and subcutaneouscontrol M-ODN; FIG. 8D, DSS and subcutaneous immunomodulatorypolynucleotide; and FIG. 8E, DSS and intragastric immunomodulatorypolynucleotide.

[0022] FIGS. 9A-9E are photographs of TUNEL assays of colon sectionstaken from control, DSS-treated, or DSS-treated and immunomodulatorypolynucleotide-treated mice. FIG. 9A, control (no DSS, nopolynucleotide); FIG. 9B, DSS alone; FIG. 9C, DSS and subcutaneouscontrol M-ODN; FIG. 9D, DSS and subcutaneous immunomodulatorypolynucleotide; and FIG. 9E, DSS and intragastric immunomodulatorypolynucleotide.

[0023]FIGS. 10A and 10B are graphs showing Caspase-3 and Caspase-9activity, respectively, in bone marrow derived macrophages cultured inmedia alone (Control, open squares), with DSS (closed squares), DSS andimmunomodulatory polynucleotide (open circles), DSS and control M-ODN(closed circles), and DSS and ZVAD, a synthetic inhibitor of caspases(open triangles).

[0024] FIGS. 11A-11F are graphs showing the effects of immunomodulatorypolynucleotide upon DNBS-induced colitis. Immunomodulatorypolynucleotide was administered subcutaneously 2 hours prior to DNBSchallenge in FIGS. 11A-E.

[0025] Immunomodulatory polynucleotide was administered 48 hrs afterDNBS challenge in FIG. 11F.

[0026] FIGS. 12A-12D are graphs showing the effects o immunomodulatorypolynucleotide upon spontaneous colitis in IL-10 knockout transgenicmice.

[0027] Immunomodulatory polynucleotide (ISS) was administered every 14days (FIG. 12C) or every 7 days (FIG. 12D). Control represents untreatedanimals (FIG. 12A). The effects of control M-ODN delivered every 7 daysare presented in FIG. 12B. The dark portion of the bars represent thenumber of animals in the group presenting with disease, while thegray-shaded portion represents the percentage of animals that werehealthy at the indicated timepoints.

[0028] FIGS. 13A-13B are graphs showing the effect of lactobacillus(VSL) genomic DNA, E. coli genomic DNA, or control calf thymus DNA(thymus) upon body weight (FIG. 13A) and disease activity index (FIG.13B) in an DSS-induced animal model of colitis.

DETAILED DESCRIPTION OF THE INVENTION

[0029] Before the present invention is described, it is to be understoodthat this invention is not limited to particular embodiments described,as such may, of course, vary. It is also to be understood that theterminology used herein is for the purpose of describing particularembodiments only, and is not intended to be limiting, since the scope ofthe present invention will be limited only by the appended claims.

[0030] Unless defined otherwise, all technical and scientific terms usedherein have the same meaning as commonly understood by one of ordinaryskill in the art to which this invention belongs. Although any methodsand materials similar or equivalent to those described herein can beused in the practice or testing of the present invention, the preferredmethods and materials are now described. All publications mentionedherein are incorporated herein by reference to disclose and describe themethods and/or materials in connection with which the publications arecited.

[0031] It must be noted that as used herein and in the appended claims,the singular forms “a”, “and”, and “the” include plural referents unlessthe context clearly dictates otherwise. Thus, for example, reference to“a cell” includes a plurality of such cells and reference to “thepolynucleotide” includes reference to one or more polynucleotides andequivalents thereof known to those skilled in the art, and so forth.

[0032] The publications discussed herein are provided solely for theirdisclosure prior to the filing date of the present application. Nothingherein is to be construed as an admission that the present invention isnot entitled to antedate such publication by virtue of prior invention.Further, the dates of publication provided may be different from theactual publication dates which may need to be independently confirmed.

DEFINITIONS

[0033] The terms “immunomodulatory nucleic acid molecule,”“immunomodulatory sequence,” “immunostimulatory sequence,” “ISS,”“ISS-PN,” and “ISS-ODN,” used interchangeably herein, refer to apolynucleotide that comprises at least one immunomodulatory nucleic acidmoiety, e.g., a sequence comprising an immunomodulatory consensussequence 5′-rrcgyy-3′. The term “immunomodulatory,” as used herein inreference to a nucleic acid molecule, refers to the ability of a nucleicacid molecule to modulate an immune response in a vertebrate host. Ingeneral the immunomodulatory sequence moiety is a single-ordouble-stranded DNA or RNA oligonucleotide having at least sixnucleotide bases that may comprise, or consist of, a modifiedoligonucleotide or a sequence of modified nucleosides. Preferably, theimmunomodulatory moieties comprise, or may be flanked by, a CGcontaining nucleotide sequence or a p(IC) nucleotide sequence, which maybe palindromic. Immunomodulatory sequences include any immunomodulatorysequence-enriched DNA, such as microbial or plasmid DNA. It should benoted that these sequences were originally identified by their activityin stimulating an immune response, and hence are referred to as an“immunostimulatory sequence” or “ISS”. However, this designation is tobe viewed as a reference that results from the history of thesepolynucleotides in the art, and is not meant to suggest that thesequences have activity only in stimulation of immune responses,particular in view of the activity of these sequences in bothsuppressing and enhancing various aspects of immune responses (e.g.,enhancing Th1-based immune responses while decreasing Th2-based immuneresponses)

[0034] The terms “oligonucleotide,” “polynucleotide,” “sequence,” and“nucleic acid molecule”, used interchangeably herein, refer to polymericforms of nucleotides of any length, either ribonucleotides ordeoxyribonucleotides. Thus, this term includes, but is not limited to,single-, double-, or multi-stranded DNA or RNA, genomic bacterial DNA,plasmid DNA, CDNA, DNA-RNA hybrids, or a polymer comprising purine andpyrimidine bases or other natural, chemically or biochemically modified,non-natural, or derivatized nucleotide bases. The backbone of thepolynucleotide can comprise sugars and phosphate groups (as maytypically be found in RNA or DNA), or modified or substituted sugar orphosphate groups. Alternatively, the backbone of the polynucleotide cancomprise a polymer of synthetic subunits such as phosphoramidites,and/or phosphorothioates, and thus can be an oligodeoxynucleosidephosphoramidate or a mixed phosphoramidate-phosphodiester oligomer.Peyrottes et al. (1996) Nucl. Acids Res. 24:1841-1848; Chaturvedi et al.(1996) Nucl. Acids Res. 24:2318-2323. The polynucleotide may compriseone or more L-nucleosides. A polynucleotide may comprise modifiednucleotides, such as methylated nucleotides and nucleotide analogs,uracyl, other sugars, and linking groups such as fluororibose andthioate, and nucleotide branches. The sequence of nucleotides may beinterrupted by non-nucleotide components. A polynucleotide may bemodified to comprise N3′-P5′ (NP) phosphoramidate, morpholinophosphorociamidate (MF), locked nucleic acid (LNA), 2′-O-methoxyethyl(MOE), or 2′-fluoro, arabino-nucleic acid (FANA), which can enhance theresistance of the polynucleotide to nuclease degradation (see, e.g.,Faria et al. (2001) Nature Biotechnol. 19:40-44; Toulme (2001) NatureBiotechnol. 19:17-18). A polynucleotide may be further modified afterpolymerization, such as by conjugation with a labeling component. Othertypes of modifications included in this definition are caps,substitution of one or more of the naturally occurring nucleotides withan analog, and introduction of means for attaching the polynucleotide toproteins, metal ions, labeling components, other polynucleotides, or asolid support. Immunomodulatory nucleic acid molecules can be providedin various formulations, e.g., in association with liposomes,microencapsulated, etc., as described in more detail herein.

[0035] As used herein the term “isolated” is meant to describe acompound of interest that is in an environment different from that inwhich the compound naturally occurs. “Isolated” is meant to includecompounds that are within samples that are substantially enriched forthe compound of interest and/or in which the compound of interest ispartially or substantially purified.

[0036] As used herein, the term “substantially purified” refers to acompound that is removed from its natural environment and is at least60% free, preferably 75% free, and most preferably 90% free from othercomponents with which it is naturally associated.

[0037] “Gastrointestinal inflammation” as used herein refers toinflammation of a mucosal layer of the gastrointestinal tract, andencompasses acute and chronic inflammatory conditions. Acuteinflammation is generally characterized by a short time of onset andinfiltration or influx of neutrophils. Chronic inflammation is generallycharacterized by a relatively longer period of onset and infiltration orinflux of mononuclear cells. Chronic inflammation can also typicallycharacterized by periods of spontaneous remission and spontaneousoccurrence. “Mucosal layer of the gastrointestinal tract” is meant toinclude mucosa of the bowel (including the small intestine and largeintestine), rectum, stomach (gastric) lining, oral cavity, and the like.

[0038] “Chronic gastrointestinal inflammation” refers to inflammation ofthe mucosal of the gastrointestinal tract that is characterized by arelatively longer period of onset, is long-lasting (e.g., from severaldays, weeks, months, or years and up to the life of the subject), and isassociated with infiltration or influx of mononuclear cells and can befurther associated with periods of spontaneous remission and spontaneousoccurrence. Thus, subjects with chronic gastrointestinal inflammationmay be expected to require a long period of supervision, observation, orcare. “Chronic gastrointestinal inflammatory conditions” (also referredto as “chronic gastrointestinal inflammatory diseases”) having suchchronic inflammation include, but are not necessarily limited to,inflammatory bowel disease (IBD), colitis induced by environmentalinsults (e.g., gastrointestinal inflammation (e.g., colitis) caused byor associated with (e.g., as a side effect) a therapeutic regimen, suchas administration of chemotherapy, radiation therapy, and the like),colitis in conditions such as chronic granulomatous disease (Schappi etal. Arch Dis Child. 2001 February;1984(2):147-151), celiac disease,celiac sprue (a heritable disease in which the intestinal lining isinflamed in response to the ingestion of a protein known as gluten),food allergies, gastritis, infectious gastritis or enterocolitis (e.g.,Helicobacter pylori-infected chronic active gastritis) and other formsof gastrointestinal inflammation caused by an infectious agent, andother like conditions.

[0039] As used herein, “inflammatory bowel disease” or “IBD” refers toany of a variety of diseases characterized by inflammation of all orpart of the intestines. Examples of inflammatory bowel disease include,but are not limited to, Crohn's disease and ulcerative colitis.Reference to IBD throughout the specification is often referred to inthe specification as exemplary of gastrointestinal inflammatoryconditions, and is not meant to be limiting.

[0040] As used herein, “subject” or “individual” or “patient” refers toany subject for whom or which therapy is desired, and generally refersto the recipient of the therapy to be practiced according to theinvention. The subject can be any vertebrate, but will preferably be amammal. If a mammal, the subject will preferably be a human, but mayalso be a domestic livestock, laboratory subject or pet animal.

[0041] “Treatment” or “treating” as used herein means any therapeuticintervention in a subject, usually a mammalian subject, generally ahuman subject, including: (i) prevention, that is, causing the clinicalsymptoms not to develop, e.g., preventing progression to a harmfulstate; (ii) inhibition, that is, arresting the development or furtherdevelopment of clinical symptoms, e.g., mitigating or completelyinhibiting active (ongoing) inflammation so as to decrease inflammation,which decrease can include substantially complete elimination ofinflammation; and/or (iii) relief, that is, causing the regression ofclinical symptoms, e.g., causing relief from diarrhea, rectal bleedingand weight loss, reduction in colon weight, reduction in colon lesions,reduction of strictures, reduction of fistulae, and/or reduction colonicinflammation.

[0042] The term “effective amount” or “therapeutically effective amount”means a dosage sufficient to provide for treatment for the disease statebeing treated or to otherwise provide the desired effect (e.g.,reduction of inflammation). The precise dosage will vary according to avariety of factors such as subject-dependent variables (e.g., age,immune system health, etc.), the disease (e.g., the type ofgastrointestinal inflammation), and the treatment being effected. In thecase of treatment of gastrointestinal inflammation, an “effectiveamount” is that amount sufficient to substantially improve thelikelihood of treating the inflammation or other symptom of agastrointestinal inflammatory disease such as IBD.

[0043] As used herein, “pharmaceutically acceptable carrier” includesany material which, when combined with an active ingredient of acomposition, allows the ingredient to retain biological activity andwithout causing disruptive reactions with the subject's immune system.Examples include, but are not limited to, any of the standardpharmaceutical carriers such as a phosphate buffered saline solution,water, emulsions such as oil/water emulsion, and various types ofwetting agents. Preferred diluents for aerosol or parenteraladministration are phosphate buffered saline or normal (0.9%) saline.Compositions comprising such carriers are formulated by well knownconventional methods (see, for example, Remington's PharmaceuticalSciences, Chapter 43, 14th Ed., Mack Publishing Col, Easton Pa. 18042,USA).

OVERVIEW

[0044] The present invention is based on the discovery that enteral andparenteral administration of immunomodulatory polynucleotide sequences(referred to herein for convenience's sake as ISS) to a subject areeffective in reducing symptoms of an inflammatory condition of thegastrointestinal tract, such as that of inflammatory bowel disease(IBD). The invention provides a new and potent therapeutic advantagethat is effective across species in a variety of animal models ofchronic and/or acute gastrointestinal inflammation, particularly inanimal models of IBD, which animal models are regarded in the field asmodels of disease in humans. Immunomodulatory nucleic acid in treatmentof gastrointestinal inflammation shown herein to reduce diseaseactivity, e.g., diarrhea, rectal bleeding and weight loss, to reducecolon weight and colon lesions, as well as to reduce colonicinflammation, as measured by, for example, anti-neutrophil cytoplasmicantibodies (ANCA), colonic myelo-peroxidase activity, or otherconventional indicator of gastrointestinal inflammation, and suchindicators can be sued to monitor immunomodulatory nucleic acid-basedtherapy as described herein. This discovery offers an attractive newtreatment strategy for the large number of patients suffering fromgastrointestinal inflammation, particularly chronic gastrointestinalinflammation, such as those patients suffering from IBD, particularlythose patients for whom no satisfactory and effective treatment iscurrently available.

NUCLEIC ACID MOLECULES COMPRISING IMMUNOMODULATORY NUCLEIC ACID MOLECULE

[0045] Nucleic acid molecules comprising an immunomodulatory nucleicacid molecule which are suitable for use in the methods of the inventioninclude an oligonucleotide, which can be a part of a larger nucleotideconstruct such as a plasmid and larger structures such as genomicbacterial DNA. The term “polynucleotide” therefore includesoligonucleotides, modified oligonucleotides and oligonucleosides, aloneor as part of a larger construct. The polynucleotide can besingle-stranded DNA (ssDNA), double-stranded DNA (dsDNA),single-stranded RNA (ssRNA) or double-stranded RNA (dsRNA). Thepolynucleotide portion can be linearly or circularly configured, or theoligonucleotide portion can contain both linear and circular segments.Immunomodulatory nucleic acid molecules also encompasses crude,detoxified bacterial (e.g., mycobacterial) RNA or DNA, as well asISS-enriched plasmids. “ISS-enriched plasmid” as used herein is meant torefer to a linear or circular plasmid that comprises or is engineered tocomprise a greater number of CpG motifs than normally found in mammalianDNA. Exemplary ISS-enriched plasmids are described in, for example,Roman et al (1997) Nat Med. 3(8):849-54. Modifications ofpolynucleotides include, but are not limited to, modifications of the3′OH or 5′OH group, modifications of the nucleotide base, modificationsof the sugar component, and modifications of the phosphate group.Bacterial DNA can also be modified as described herein for use in theinvention.

[0046] The immunomodulatory nucleic acid molecule can compriseribonucleotides (containing ribose as the only or principal sugarcomponent), deoxyribonucleotides (containing deoxyribose as theprincipal sugar component), or in accordance with the establishedstate-of-the-art, modified sugars or sugar analogs may be incorporatedin the oligonucleotide of the present invention. Examples of a sugarmoiety that can be used include, in addition to ribose and deoxyribose,pentose, deoxypentose, hexose, deoxyhexose, glucose, arabinose, xylose,lyxose, and a sugar “analog” cyclopentyl group. The sugar may be inpyranosyl or in a furanosyl form. In the modified oligonucleotides ofthe present invention, the sugar moiety is preferably the furanoside ofribose, deoxyribose, arabinose or 2′-O-methylribose, and the sugar maybe attached to the respective heterocyclic bases either in I or Janomeric configuration.

[0047] An immunomodulatory nucleic acid molecule may comprise at leastone nucleoside comprising an L-sugar. The L-sugar may be deoxyribose,ribose, pentose, deoxypentose, hexose, deoxyhexose, glucose, galactose,arabinose, xylose, lyxose, or a sugar “analog” cyclopentyl group. TheL-sugar may be in pyranosyl or furanosyl form.

[0048] The phosphorous derivative (or modified phosphate group) that canbe attached to the sugar or sugar analog moiety in the modifiedoligonucleotides of the present invention can be a monophosphate,diphosphate, triphosphate, alkylphosphate, alkanephosphate,phosphorothioate, phosphorodithioate or the like. The heterocyclicbases, or nucleic acid bases that are incorporated in theoligonucleotide base of the ISS can be the naturally occurring principalpurine and pyrimidine bases, (namely uracil or thymine, cytosine,adenine and guanine, as mentioned above), as well as naturally occurringand synthetic modifications of said principal bases. Those skilled inthe art will recognize that a large number of “synthetic” non-naturalnucleosides comprising various heterocyclic bases and various sugarmoieties (and sugar analogs) are available, and that theimmunomodulatory nucleic acid molecule can include one or severalheterocyclic bases other than the principal five base components ofnaturally occurring nucleic acids. Preferably, however, the heterocyclicbase in the ISS is selected from uracil-5-yl, cytosin-5-yl, adenin-7-yl,adenin-8-yl, guanin-7-yl, guanin-8-yl, 4-aminopyrrolo [2,3-d]pyrimidin-5-yl, 2-amino-4-oxopyrolo [2,3-d] pyrimidin-5-yl,2-amino-4-oxopyrrolo [2,3-d] pyrimidin-3-yl groups, where the purinesare attached to the sugar moiety of the oligonucleotides via the9-position, the pyrimidines via the 1-position, the pyrrolopyrimidinesvia the 7-position and the pyrazolopyrimidines via the 1-position.

[0049] Structurally, the root oligonucleotide of the immunomodulatorynucleic acid molecule is a non-coding sequence that can include at leastone unmethylated CpG motif. The relative position of any CpG sequence inISS with immunomodulatory activity in certain mammalian species (e.g.,rodents) is 5′-CG-3′ (i.e., the C is in the 5′ position with respect tothe G in the 3′ position).

[0050] Immunomodulatory nucleic acid molecules generally do not providefor, nor is there any requirement that they provide for, expression ofany amino acid sequence encoded by the polynucleotide, and thus thesequence of a immunomodulatory nucleic acid molecule may be, andgenerally is, non-coding. Immunomodulatory nucleic acid molecules maycomprise a linear double or single-stranded molecule, a circularmolecule, or can comprise both linear and circular segments.Immunomodulatory nucleic acid molecules may be single-stranded, or maybe completely or partially double-stranded.

[0051] In some embodiments, an immunomodulatory nucleic acid molecule isan oligonucleotide, e.g., has a sequence of from about 6 to about 200,from about 10 to about 100, from about 12 to about 50, or from about 15to about 25, nucleotides in length.

[0052] Exemplary consensus CpG motifs of immunomodulatory nucleic acidmolecules useful in the invention include, but are not necessarilylimited to:

[0053] 5′-Purine-Purine-[C]-[G]-Pyrimidine-Pyrimidine-3′, in which theimmunomodulatory nucleic acid molecule comprises a CpG motif flanked byat least two purine nucleotides (e.g., GG, GA, AG, AA, II, etc.,) and atleast two pyrimidine nucleotides (CC, TT, CT, TC, UU, etc.);

[0054] 5′-Purine-TCG-Pyrimidine-Pyrimidine-3′;

[0055] 5′-[TCG]_(n)-3′, where n is any integer that is 1 or greater,e.g., to provide a poly-TCG immunomodulatory nucleic acid molecule(e.g., where n=3, the polynucleotide comprises the sequence5′-TCGTCGTCG-3′);

[0056] 5′-Purine-Purine-CG-Pyrimidine-Pyrimidine-CG-3′; and

[0057] 5′-Purine-TCG-Pyrimidine-Pyrimidine-CG-3′

[0058] Exemplary DNA-based immunomodulatory nucleic acid moleculesuseful in the invention include, but are not necessarily limited to,polynucleotides comprising the following nucleotide sequences: AACGCC,AACGCT, ACGTC, AACGTT; AGCGCC, AGCGCT, AGCGTC, AGCGTT; GACGCC, GACGCT,GACGTC, GACGTT; GGCGCC, GGCGCT, GGCGTC, GGCGTT; ATCGCC, ATCGCT, ATCGTC,ATCGTT; GTCGCC, GTCGCT, GTCGTC, GTCGTT; and TCGTCG, and TCGTCGTCG.

[0059] Octameric sequences are generally the above-mentioned hexamericsequences, with an additional 3′ CG. Exemplary DNA-basedimmunomodulatory nucleic acid molecules useful in the invention include,but are not necessarily limited to, polynucleotides comprising thefollowing octameric nucleotide sequences: AACGCCCG, AACGCTCG, AACGTCCG,AACGTTCG; AGCGCCCG, AGCGCTCG, AGCGTCCG, AGCGTTCG; GACGCCCG, GACGCTCG,GACGTCCG, GACGTTCG; GGCGCCCG, GGCGCTCG, GGCGTCCG, GGCGTTCG; ATCGCCCG,ATCGCTCG, ATCGTCCG, ATCGTTCG; GTCGCCCG, GTCGCTCG, GTCGTCCG, andGTCGTTCG.

[0060] Immunomodulatory nucleic acid molecules useful in the inventioncan comprise one or more of any of the above CpG motifs. For example,immunomodulatory nucleic acid molecules useful in the invention cancomprise a single instance or multiple instances (e.g., 2, 3, 5 or more)of the same CpG motif. Alternatively, the immunomodulatory nucleic acidmolecules can comprises multiple CpG motifs (e.g., 2, 3, 5 or more)where at least two of the multiple CpG motifs have different consensussequences, or where all CpG motifs in the immunomodulatory nucleic acidmolecules have different consensus sequences.

[0061] A non-limiting example of an immunomodulatory nucleic acidmolecule is one with the sequence 5′-TGACTGTGAACGTTCGAGATGA-3′ (SEQ IDNO:1). An example of a control nucleic acid molecule is one having thesequence 5′- TGACTGTGTTCCTTAGAGATGA-3′ (SEQ ID NO:2), which differs fromSEQ ID NO: 1 at the nucleotide indicated in lower case type.

[0062] Immunomodulatory nucleic acid molecules useful in the inventionmay or may not include palindromic regions. If present, a palindrome mayextend only to a CpG motif, if present, in the core hexamer or octamersequence, or may encompass more of the hexamer or octamer sequence aswell as flanking nucleotide sequences.

[0063] The core hexamer structure of the foregoing immunomodulatorynucleic acid molecules can be flanked upstream and/or downstream by anynumber or composition of nucleotides or nucleosides. However,immunomodulatory nucleic acid are generally at least 6 bases in length,and preferably are between 6 and 200 bases in length, to enhance uptakeof the immunomodulatory nucleic acid molecule into target tissues.

[0064] In particular, immunomodulatory nucleic acid molecules useful inthe invention include those that have hexameric nucleotide sequenceshaving “CpG” motifs. Although DNA sequences are generally preferred, RNAimmunomodulatory nucleic acid molecules can be used, with inosine and/oruracil substitutions for nucleotides in the hexamer sequences.

MODIFICATIONS

[0065] Immunomodulatory nucleic acid molecules can be modified in avariety of ways. For example, the immunomodulatory nucleic acidmolecules can comprise backbone phosphate group modifications (e.g.,methylphosphonate, phosphorothioate, phosphoroamidate andphosphorodithioate internucleotide linkages), which modifications can,for example, enhance stability of the immunomodulatory nucleic acidmolecule in vivo, making them particularly useful in therapeuticapplications. A particularly useful phosphate group modification is theconversion to the phosphorothioate or phosphorodithioate forms of animmunomodulatory nucleic acid molecule. Phosphorothioates andphosphorodithioates are more resistant to degradation in vivo than theirunmodified oligonucleotide counterparts, increasing the half-lives ofthe immunomodulatory nucleic acid molecules and making them moreavailable to the subject being treated.

[0066] Other modified immunomodulatory nucleic acid moleculesencompassed by the present invention include immunomodulatory nucleicacid molecules having modifications at the 5′ end, the 3′ end, or boththe 5+ and 3′ ends. For example, the 5′ and/or 3′ end can be covalentlyor non-covalently conjugated to a molecule (either nucleic acid,non-nucleic acid, or both) to, for example, increase thebio-availability of the immunomodulatory nucleic acid molecules,increase the efficiency of uptake where desirable, facilitate deliveryto cells of interest, and the like. Exemplary molecules for conjugationto the immunomodulatory nucleic acid molecules include, but are notnecessarily limited to, cholesterol, phospholipids, fatty acids,sterols, oligosaccharides, polypeptides (e.g., immunoglobulins),peptides, antigens (e.g., peptides, small molecules, etc.), linear orcircular nucleic acid molecules (e.g., a plasmid), and the like.Additional immunomodulatory nucleic acid conjugates, and methods formaking same, are known in the art and described in, for example, WO98/16427 and WO 98/55495. Thus, the term “immunomodulatory nucleic acidmolecule” includes conjugates comprising an immunomodulatory nucleicacid molecule.

PREPARATION OF IMMUNOMODULATORY NUCLEIC ACID MOLECULES

[0067] Immunomodulatory nucleic acid molecules can be synthesized usingtechniques and nucleic acid synthesis equipment well known in the art(see, e.g., Ausubel et al. Current Protocols in Molecular Biology,(Wiley Intersicence, 1989); Maniatis et al. Molecular Cloning: ALaboratory Manual (Cold Spring Harbor Laboratories, New York, 1982); andU.S. Pat. Nos. 4,458,066; and 4,650,675. Individual polynucleotidefragments can be ligated with a ligase such as T4 DNA or RNA ligase asdescribed in, e.g., U.S. Pat. No. 5,124,246. Oligonucleotide degradationcan be accomplished through exposure to a nuclease, see, e.g., U.S. Pat.No. 4,650,675. As noted above, since the immunomodulatory nucleic acidmolecules need not provide for expression of any encoded amino acidsequence, the invention does not require that the immunomodulatorynucleic acid molecules be operably linked to a promoter or otherwiseprovide for expression of a coding sequence.

[0068] Alternatively, immunomodulatory nucleic acid molecules can bepurified from E. coli or Lactobacillus, isolated from microbial species(e.g., mycobacteria) using techniques well known in the art such aspurification of genomic DNA, nucleic acid hybridization, amplification(e.g., by PCR), and the like. Isolated immunomodulatory nucleic acidmolecules can be purified to a substantially pure state, e.g., free ofendogenous contaminants, e.g., lipopolysaccharides. Immunomodulatorynucleic acid molecules isolated as part of a larger polynucleotide canbe reduced to the desired length by techniques well known in the art,such as endonuclease digestion. Other techniques suitable for isolation,purification, and production of polynucleotides to obtain ISS will bereadily apparent to the ordinarily skilled artisan in the relevantfield.

[0069] Circular immunomodulatory nucleic acid molecules can also besynthesized through recombinant methods or chemically synthesized. Wherecircular immunomodulatory nucleic acid molecules are obtained throughisolation or recombinant methods, the immunomodulatory nucleic acidmolecule can be provided as a plasmid. Chemical synthesis of smallercircular oligonucleotides can be performed using methods known in theart (see, e.g., Gao et al. (1995) Nucl. Acids. Res. 23:2025-9; Wang etal., (1994) Nucl. Acids Res. 22:2326-33).

[0070] Where the immunomodulatory nucleic acid molecule comprises amodified oligonucleotide, the modified oligonucleotides can besynthesized using standard chemical techniques. For example,solid-support based construction of methylphosphonates has beendescribed in Agrawal et al. Tet. Lett. 28:3539-42. Synthesis of otherphosphorous-based modified oligonucleotides, such as phosphotriesters(see, e.g., Miller et al. (1971) J. Am Chem Soc. 93:6657-65),phosphoramidates (e.g., Jager et al. (1988) Biochem. 27:7237-46), andphosphorodithioates (e.g., U.S. Pat. No. 5,453,496) is known in the art.Other non-phosphorous-based modified oligonucleotides can also be used(e.g., Stirchak et al. (1989) Nucl. Acids. Res. 17:6129-41).

[0071] Preparation of base-modified nucleosides, and the synthesis ofmodified oligonucleotides using such base-modified nucleosides asprecursors is well known in the art, see, e.g., U.S. Pat. Nos.4,910,300; 4,948,882; and 5,093,232. These base-modified nucleosideshave been designed so that they can be incorporated by chemicalsynthesis into either terminal or internal positions of anoligonucleotide. Nucleosides modified in their sugar moiety have alsobeen described (see, e.g., U.S. Pat. Nos. 4,849,513; 5,015,733;5,118,800; and 5,118,802).

[0072] Techniques for making phosphate group modifications tooligonucleotides are known in the art. Briefly, an intermediatephosphate triester for the target oligonucleotide product is preparedand oxidized to the naturally-occurring phosphate triester with aqueousiodine or other agents, such as anhydrous amines. The resultingoligonucleotide phosphoramidates can be treated with sulfur to yieldphosphorothioates.

[0073] The same general technique (without the sulfur treatment step)can be used to produced methylphosphoamidites from methylphosphonates.Techniques for phosphate group modification are well known and aredescribed in, for example, U.S. Pat. Nos. 4,425,732; 4,458,066;5,218,103; and 5,453,496.

IDENTIFICATION OF IMMUNOMODULATORY NUCLEIC ACID MOLECULES

[0074] Confirmation that a particular compound has the properties of animmunomodulatory nucleic acid molecule useful in the invention can beobtained by evaluating whether the immunomodulatory nucleic acidmolecule elicits the appropriate cytokine secretion patterns, e.g., acytokine secretion pattern associated with a type-I immune response;decreases inflammation associated with gastrointestinal inflammation(e.g., in an animal model), and the like.

[0075] In general, helper T (Th) cells are divided into broad groupsbased on their specific profiles of cytokine production: Th1, Th2, andTh0. “Th1” cells are T lymphocytes that release predominantly thecytokines IL-2 and IFN-y, which cytokines in turn promote T cellproliferation, facilitate macrophage activation, and enhance thecytolytic activity of natural killer (NK) cells and antigen-specificcytotoxic T cells (CTL). In contrast, the cytokines predominantlyreleased by Th2 cells are IL-4, IL-5, and IL-13. IL-4 and IL-5 are knownto mediate antibody isotype switching towards IgE or IgA response, andpromote eosinophil recruitment, skewing the immune system toward an“allergic” type of response. Th0 cells release a set of cytokines withcharacteristics of both Th1-type and Th2-type responses. While thecategorization of T cells as Th1, TH2, or Th0 is helpful in describingthe differences in immune response, it should be understood that it ismore accurate to view the T cells and the responses they mediate asforming a continuum, with Th1 and Th2 cells at opposite ends of thescale, and Th0 cells providing the middle of the spectrum. Therefore, itshould be understood that the use of these terms herein is only todescribe the predominant nature of the immune response elicited, and isnot meant to be limiting to an immune response that is only ofthe typeindicated. Thus, for example, reference to a “type-1” or “Th1” immuneresponse is not meant to exclude the presence of a “type-2” or “Th2”immune response, and vice versa.

[0076] Details of in vitro and in vivo techniques useful for evaluationof production of cytokines associated with a type-1 or type-2 response,as well as for evaluation of antibody production, are well known in theart. Likewise, animal models for screening candidate sequences foractivity in, for example, reduction of IBD-associated inflammation arealso well known in the art, and are further exemplified in the Examplesbelow.

ADMINISTRATION AND DOSAGE

[0077] Treatment includes prophylaxis and therapy. Prophylaxis ortherapy can be accomplished by a single direct administration at asingle time point or multiple time points. Administration can also bedelivered to a single or to multiple sites.

[0078] The subject can be any vertebrate, but will preferably be amammal. Mammals include, but are not necessarily limited to, human,bovine, equine, canine, feline, porcine, and ovine animals. If a mammal,the subject will generally be a human, but may also be a domesticlivestock, laboratory subject or pet animal. Immunomodulatory nucleicacid molecules are administered to an individual using any availablemethod and route suitable for drug delivery including systemic, mucosal,and localized routes of administration. In general, subjects who receivetherapy according to the invention include those who has or are at riskof acute or chronic gastrointestinal inflammation, particularly thosewho have or are at risk of chronic gastrointestinal inflammation,particularly inflammatory bowel disease, especially ulcerative colitisor Crohn's disease. Methods for identification of such subjects withthese conditions or at risk of these conditions are well within theskill and knowledge of the ordinarily skilled artisan.

[0079] Routes of administration, dosages, and formulations are describedin more detail below.

[0080] Routes of administration

[0081] Conventional and pharmaceutically acceptable routes ofadministration for treatment of gastrointestinal inflammation (e.g.,chronic gastrointestinal inflammation such as that of IBD), include, butare not necessarily limited to, intramuscular, subcutaneous,intradermal, transdermal, intravenous, rectal(e.g., enema, suppository),oral, intragastric, intranasal and other routes of effective inhalationroutes, and other parenteral routes of administration. In general,gastrointestinal routes of administration are of particular interest inthe present invention for treatment of gastrointestinal inflammationincluding, but not necessarily limited to oral, intranasal,intragastric, and rectal administration. Routes of administration may becombined, if desired, or adjusted depending upon the immunomodulatorynucleic acid molecule and/or the desired effect on the immune response.The immunomodulatory nucleic acid composition can be administered in asingle dose or in multiple doses, and may encompass administration ofadditional doses, to elicit and/or maintain the desired effect.

[0082] Immunomodulatory nucleic acid molecules can be administered to asubject using any available conventional methods and routes suitable fordelivery of conventional drugs, including systemic or localized routes.Methods and localized routes that further facilitate production of atype-1 or type-1-like response and/or the anti-gastrointestinalinflammatory (e.g., anti-IBD) activity of the immunomodulatory nucleicacid molecules, particularly at or near a site of inflammation is ofinterest in the invention, and may be preferred over systemic routes ofadministration, both for the immediacy of therapeutic effect andreduction of the incident of in vivo degradation of the administeredimmunomodulatory nucleic acid molecules. In general, routes ofadministration contemplated by the invention include, but are notnecessarily limited to, gastroenteral, enteral, or parenteral routes.Gastroenteral routes of administration include, but are not necessarilylimited to, oral and rectal (e.g., using a suppository) delivery.

[0083] Dose

[0084] The dose of immunomodulatory nucleic acid administrated to asubject, in the context of the present invention, should be sufficientto effect a beneficial therapeutic response in the subject over time, orto alleviate symptoms. Thus, immunomodulatory nucleic acid isadministered to a patient in an amount sufficient to alleviate, reduce,cure or at least partially arrest symptoms and/or complications from thedisease. An amount adequate to accomplish this is defined as a“therapeutically effective dose.”

[0085] A particular advantage of therapy using immunomodulatory nucleicacid according to the invention is the capacity of immunomodulatorynucleic acid to exert immunomodulatory activity even at relativelyminute dosages. Although the dosage used will vary depending on theclinical goals to be achieved, a suitable dosage range is one whichprovides up to about 1 μg, to about 1,000 μg, to about 5,000 μg, toabout 10,000 ,μg, to about 25,000 μg or about 50,000 μg ofimmunomodulatory nucleic acid per ml of carrier in a single dosage.Based on current studies, immunomodulatory nucleic acid is believed tohave little or no toxicity at these dosage levels.

[0086] It should be noted that the anti-inflammatory andimmunotherapeutic activity of immunomodulatory nucleic acid in theinvention is essentially dose-dependent. Therefore, to increaseimmunomodulatory nucleic acid potency by a magnitude of two, each singledose is doubled in concentration. Clinically, it may be advisable toadminister the immunomodulatory nucleic acid in a low dosage, thenincrease the dosage as needed to achieve the desired therapeutic goal(e.g., increasing amounts of immunomodulatory nucleic acid can beadministered until a reduction or mitigation in the gastrointestinalinflammation-associated symptom is achieved). In addition, some routesof administration will require higher concentrations than other routes.Those skilled in the art can adjust the dosage and concentration to suitthe particular route of delivery.

[0087] The effectiveness of therapy can be monitored by monitoring thereduction of disease activity in the subject. Reduction in diseaseactivity can be monitored by, for example, monitoring reduction ofincidence of diarrhea or volume of stool, reduction of rectal bleeding,reduction of weight loss, reduction of size or number of colon lesions,reduction or opening of strictures, reduction or closure of fistulae,and the like. Therapeutic effectiveness can also be measured by forexample, a decrease in anti-neutrophil cytoplasmic antibodies (ANCA) ina biological sample, a decrease in colonic myelo-peroxidase activity,reduction of anemia (as detected by, for example, erythrocytesedimentation rate (ESR), hemoglobin levels, and the like ), or otherconventional indicator of gastrointestinal inflammation. Many of thesemethods for assessing therapeutic efficacy can be accomplished throughendoscopy or through blood tests. Methods for monitoringgastrointestinal inflammation are well known in the art and well withinthe skill and knowledge of the ordinarily skilled artisan.

Reduction of Risk of Subsequent Disease

[0088] The methods of the invention can also provide for reduced risk ofother conditions for which gastrointestinal inflammation is a riskfactor. For example, ulcerative colitis is a risk factor for coloniccarcinoma. Thus, treatment of ulcerative colitis (e.g., by reduction ofinflammation) according to the methods of the invention also reduces therisk of colonic cancer (e.g., colonic carcinoma, colonic adenoma, andthe like). The methods of the invention can thus be applied asprophylactic measure to prevent or reduce the risk of onset of coloniccarcinoma, particularly in those patients that are high risk of coloncancer.

[0089] Established risk factors for colon cancer in those patientshaving ulcerative colitis include long duration of the disease, largeextent of the disease, low activity of the disease, young age at onset,presence of complicating primary sclerosing cholangitis or stenoticdisease and possibly lack of adequate surveillance, inadequatepharmacological therapy, folate deficiency and non-smoking. Crohn'sdisease is associated with an increased risk of colorectal carcinoma inpatients with long-standing disease, strictures and fistulae under thecondition that the colon is involved, tumors of the small intestine mayoccur occasionally. (see, e.g., Pohl, et al. (2000), ibid). Thustreating using immunomodulatory nucleic acid according to the inventioncan be of particular benefit in these patients.

[0090] Formulations

[0091] In general, immunomodulatory nucleic acid molecules are preparedin a pharmaceutically acceptable composition for delivery to a host.Immunomodulatory nucleic acid are optionally provided with apharmaceutically acceptable carrier. Exemplary pharmaceutically carriersinclude sterile aqueous of non-aqueous solutions, suspensions, andemulsions. Examples of non-aqueous solvents are propylene glycol,polyethylene glycol, vegetable oils such as olive oil, and injectableorganic esters such as ethyl oleate. Aqueous carriers include water,alcoholic/aqueous solutions, emulsions or suspensions, including salineand buffered media. Parenteral vehicles include sodium chloridesolution, Ringer's dextrose, dextrose and sodium chloride, lactatedRinger's or fixed oils. Intravenous vehicles include fluid and nutrientreplenishers, electrolyte replenishers (such as those based on Ringer'sdextrose), and the like. A composition of immunomodulatory nucleic acidmay also be lyophilized using means well known in the art, forsubsequent reconstitution and use according to the invention. Also ofinterest are formulations for liposomal delivery, and formulationscomprising microencapsulated immunomodulatory nucleic acid molecules.

[0092] In general, the pharmaceutical compositions can be prepared invarious forms, such as granules, tablets, pills, suppositories, capsules(e.g. adapted for oral delivery), microbeads, microspheres, liposomes,suspensions, salves, lotions and the like. The immunomodulatory nucleicacid useful in the invention can be prepared in a variety offormulations, including conventional pharmaceutically acceptablecarriers, and, for example.

[0093] Pharmaceutical grade organic or inorganic carriers and/ordiluents suitable for oral and topical use can be used to make upcompositions comprising the therapeutically-active compounds. Diluentsknown to the art include aqueous media, vegetable and animal oils andfats. Stabilizing agents, wetting and emulsifying agents, salts forvarying the osmotic pressure or buffers for securing an adequate pHvalue,.

[0094] Immunomodulatory nucleic acid molecules can be administered inthe absence of agents or compounds that might facilitate uptake bytarget cells (e.g., as a “naked” polynucleotide, e.g., a polynucleotidethat is not encapsulated by a viral particle). Immunomodulatory nucleicacid molecules can also be administered with compounds that facilitateuptake of immunomodulatory nucleic acid molecules by cells (e.g., bymacrophages) or otherwise enhance transport of the immunomodulatorynucleic acid molecules to a treatment site for action.

[0095] Absorption promoters, detergents and chemical irritants (e.g.,keratinolytic agents) can enhance transmission of an immunomodulatorynucleic acid molecule composition into a target tissue (e.g., throughthe skin). For general principles regarding absorption promoters anddetergents which have been used with success in mucosal delivery oforganic and peptide-based drugs, see, e.g., Chien, Novel Drug DeliverySystems, Ch. 4 (Marcel Dekker, 1992). Suitable agents which are known toenhance absorption of drugs through skin are described in Sloan, Use ofSolubility Parameters from Regular Solution Theory to DescribePartitioning-Driven Processes, Ch. 5, “Prodrugs: Topical and Ocular DrugDelivery” (Marcel Dekker, 1992), and at places elsewhere in the text.All of these references are incorporated herein for the sole purpose ofillustrating the level of knowledge and skill in the art concerning drugdelivery techniques.

[0096] A colloidal dispersion system may be used for targeted deliveryof immunomodulatory nucleic acid molecules to specific tissue. Colloidaldispersion systems include macromolecule complexes, nanocapsules,microspheres, beads, and lipid-based systems including oil-in-wateremulsions, micelles, mixed micelles, and liposomes.

[0097] Liposomes are artificial membrane vesicles which are useful asdelivery vehicles in vitro and in vivo. It has been shown that largeunilamellar vesicles (LUV), which range in size from 0.2-4.0 μm canencapsulate a substantial percentage of an aqueous buffer containinglarge macromolecules. RNA and DNA can be encapsulated within the aqueousinterior and be delivered to cells in a biologically active form(Fraley, et al., (1981) Trends Biochem. Sci., 6:77). The composition ofthe liposome is usually a combination of phospholipids, particularlyhigh-phase-transition-temperature phospholipids, usually in combinationwith steroids, especially cholesterol. Other phospholipids or otherlipids may also be used. The physical characteristics of liposomesdepend on pH, ionic strength, and the presence of divalent cations.Examples of lipids useful in liposome production include phosphatidylcompounds, such as phosphatidylglycerol, phosphatidylcholine,phosphatidylserine, phosphatidylethanolamine, sphingolipids,cerebrosides, and gangliosides. Particularly useful arediacylphosphatidylglycerols, where the lipid moiety contains from 14-18carbon atoms, particularly from 16-18 carbon atoms, and is saturated.Illustrative phospholipids include egg phosphatidylcholine,dipalmitoylphosphatidylcholine and distearoylphosphatidylcholine.

[0098] Where desired, targeting of liposomes can be classified based onanatomical and mechanistic factors. Anatomical classification is basedon the level of selectivity, for example, organ-specific, cell-specific,and organelle-specific. Mechanistic targeting can be distinguished basedupon whether it is passive or active. Passive targeting utilizes thenatural tendency of liposomes to distribute to cells of thereticulo-endothelial system (RES) in organs which contain sinusoidalcapillaries. Active targeting, on the other hand, involves alteration ofthe liposome by coupling the liposome to a specific ligand such as amonoclonal antibody, sugar, glycolipid, or protein, or by changing thecomposition or size of the liposome in order to achieve targeting toorgans and cell types other than the naturally occurring sites oflocalization.

[0099] The surface of the targeted delivery system may be modified in avariety of ways. In the case of a liposomal targeted delivery system,lipid groups can be incorporated into the lipid bilayer of the liposomein order to maintain the targeting ligand in stable association with theliposomal bilayer. Various well known linking groups can be used forjoining the lipid chains to the targeting ligand (see, e.g., Yanagawa,et al., (1988) Nuc. Acids Symp. Ser., 19:189; Grabarek, et al., (1990)Anal. Biochem., 185:131; Staros, et al., (1986) Anal. Biochem. 156:220and Boujrad, et al., (1993) Proc. Natl. Acad. Sci. USA, 90:5728).Targeted delivery of immunomodulatory nucleic acid molecules can also beachieved by conjugation of the ISS to the surface of viral and non-viralrecombinant expression vectors, to an antigen or other ligand, to amonoclonal antibody or to any molecule which has the desired bindingspecificity.

[0100] Additional Agents

[0101] Immunomodulatory nucleic acid for delivery according to theinvention can be formulated with additional agents, which agents may beinert or active agents. For example, preservatives and other additivesmay also be present such as, for example, antimicrobial agents (e.g.,antibacterials, antivirals, antifungals, etc.), antioxidants, chelatingagents, and inert gases and the like. In addition, the immunomodulatorynucleic acid may be modified to be conjugated to another molecule ofinterest.

[0102] Immunomodulatory nucleic acid can be combined with conventionalagents used for treatment of gastrointestinal inflammation, whereappropriate. Exemplary agents used in conventional gastrointestinalinflammation therapy, such as those used in therapy for chronicgastrointestinal inflammation such as in IBD, include, but are notnecessarily limited to, corticosteroids, azathioprine, cyclosporine, andmethotrexate, as well as antibodies directed against tumor necrosisfactor-α (TNF-α), or other drug useful in the treatment of chronicgastrointestinal inflammation. Such additional agents can beadministered separately or included in the immunomodulatory nucleic acidcomposition. In addition immunomodulatory nucleic acid can be formulatedwith other anti-inflammatory agents, with the proviso that such agentsdo not substantially interfere with the anti-inflammatory activity ofimmunomodulatory nucleic acid. Exemplary agents include, but are notnecessarily limited to, antacids, H2 blockers, and the like (e.g.,famotidine, ranitidine hydrochloride, and the like).

[0103] Timing of Administration

[0104] Immunomodulatory nucleic acid molecules can be administered to asubject prior to onset of more severe symptoms (e.g., prior to onset ofan acute inflammatory attack), or after onset of acute or chronicsymptoms (e.g., after onset of an acute inflammatory attack). As such,immunomodulatory nucleic acids can be administered at any time, and maybe administered at any interval. In one embodiment, immunomodulatorynucleic acid is administered about 8 hours, about 12 hours, about 24hours, about 2 days, about 4 days, about 8 days, about 16 days, about 30days or 1 month, about 2 months, about 4 months, about 8 months, orabout 1 year after initial onset of gastrointestinalinflammation-associated symptoms and/or after diagnosis ofgastrointestinal inflammation in the subject. As described in moredetail below, the invention also provides for administration ofsubsequent doses of immunomodulatory nucleic acid molecules.

[0105] When multiple doses are administered, subsequent doses areadministered within about 16 weeks, about 12 weeks, about 8 weeks, about6 weeks, about 4 weeks, about 2 weeks, about 1 week, about 5 days, about72 hours, about 48 hours, about 24 hours, about 12 hours, about 8 hours,about 4 hours, or about 2 hours or less of the previous dose. In oneembodiment, ISS are administered at intervals ranging from at leastevery two weeks to every four weeks (e.g., monthly intervals) in orderto maintain the maximal desired therapeutic effect (e.g., to provide formaintenance of relief from IBD-associated symptoms).

[0106] In view of the teaching provided by this disclosure, those ofordinary skill in the clinical arts will be familiar with, or canreadily ascertain, suitable parameters for administration ofimmunomodulatory nucleic acid according to the invention.

EXAMPLES

[0107] The following examples are presented to illustrate the presentinvention and to assist one of ordinary skill in making and using thesame. The examples are not intended in any way to otherwise limit thescope of the invention.

Example 1 Subcutaneous Administration Of ISS Ameliorates Symptoms In AMouse Model Of Colitis (DSS-Induced)

[0108] In an experiment similar to that of Example 1, groups of Balb/cmice (at least 6 animals per group) were weighed and treated with ISS(10 μg/animal) or M-ODN (10 μg/animal) subcutaneously two hrs prior toinduction of colitis by adding dextran sodium sulfate (DSS, Sigma), 2.5%to the drinking water ad libitum. M-ODN is a polynucleotide of the samelength as the ISS polynucleotide, but lacking the CpG motif. Thepolynucleotides used were LPS free, single stranded, 22 mer long,phosphothioate polynucleotides (Trilink, San Diego, Calif.), and had thefollowing sequences:

[0109] ISS: 5′-TGACTGTGAACGTTCGAGATGA-3′ (SEQ ID NO:1) and

[0110] M-ODN: 5′-TGACTGTGAACCTTAG AGATGA-3′ (SEQ ID NO:3).

[0111] Naïve control animals (naïve) received neither DSS norpolynucleotide. Colitis control animals (DSS) received nopolynucleotide.

[0112] Seven days after induction of colitis, mice were weighed andinspected for diarrhea and rectal bleeding. The mice were sacrificed,and the entire colon was dissected and its length measured and weighed.Scores were again defined as follows: Changes in body weight: No loss-0; 5 to 10%-1; 10 to 25%,-2; 15 to 20%, -3; >20% 4. Hemoccult: Noblood, - 0; positive, -2; gross blood, -4. Mucosal samples wereprocessed for determination of MPO activity according to: Bradley JInvest Dermatol 78: 206-9.

[0113] As shown in FIGS. 1A-1D, a single subcutaneous administration ofISS resulted ina decrease in disease activity index (DAI)m (FIG. 1A),the percentage decrease in body weight (FIG. 1B), the colonic weight(FIG. 1C), as well as the decrease in mucosal MPO activity (FIG. 1D).

Example 2 Effect of Various Immunomodulatory Nucleic Acid Sequences onDisease Activity Index in DSS-Induced Colitis

[0114] ISS (10 μg/animal) mutated control polynucleotides (M-ODN) (10μg/animal) were injected subcutaneously in Balb/C mice 2 hours prior toDSS administration (2.5%) to drinking water as described in Example 1.The sequences of the various polynucleotides were as follows: TABLE 1SEQ ID Polynucleotide Sequence NO: 1018 tgactgtgaacgttcgagatga 1 1019tgactgtgaaggttagagatga 4 1038 tgactgtgaacgttagagatga 5 1039tgactgtgaac*gttagagatga 6 1042 tgactgtgttccttagagatga 2 1185tccatgacgttcctgatgct 7 1394 tgactgtgaatgttagagatga 8 1399tgactgtggtcgttagagatga 9 1401 tcgtcgtcgtcgtcgtcgtcgt 10  1402tgaaacgttcgcctgtcgttga 11 

[0115] Mice were sacrificed 7 days after DSS administration, and diseaseactivity index evaluated. The disease activity index was measured as acombined score of decrease in body weight and the presence of blood inthe stool, as described above.

[0116] Results are shown in FIG. 2.

Example 3 Dose-Response of Subcutaneous ISS in an animal model ofulcerative colitis (DSS-induced)

[0117] ISS was administered to Balb/c mice subcutaneously as describedin Example 1 above at varying doses (0 μg/animal, 3 μg/animal, and 10μg/animal). Two hours later, DSS was administered by addition to thedrinking water ad libitum at a concentration of 2.5%. Seven days afterinduction of colitis, mice were weighed and inspected for diarrhea andrectal bleeding. The mice were sacrificed, and the entire colon wasdissected and its length measured and weighed. Scores were again definedas described in Example 2. The results are provided in FIGS. 3A-3C.

Example 4 Administration of ISS After Onset of Colitis in an AnimalModel (DSS-induced)

[0118] DSS was used to induce colitis in Balb/c mice as described inExample 1. ISS or M-ODN (as described in Example 1) was administered at10 μg/animal 48 hours after DSS exposure. Naive control animals (naïve)received neither DSS nor polynucleotide. Naïve control animals (naïve)received neither DSS nor polynucleotide. Colitis control animals (DSS)received no polynucleotide.

[0119] Seven days after induction of colitis, mice were weighed andinspected for diarrhea and rectal bleeding. The mice were sacrificed,and the entire colon was dissected and its length measured and weighed.Scores were defined as in Example 1.

[0120] The results of the effect of ISS administration 48 hrs after DSSexposure are shown in FIG. 4. These results show that, in addition toits protective effects, ISS is also effective in significantlydecreasing disease activity index after onset of colitis.

Example 5 ISS in Subsequent DSS Challenge

[0121] To evaluate whether the protective effects of ISS on DSS-inducedcolitis would also protect from subsequent DSS challenge, animals werepre-treated once with ISS (10 μg/animal; ISS as described in Example 1)and exposed to DSS in water (2.5%) for one week. The protective effectsof ISS in this group (e.g., disease activity index (DAI)<1) were similarto those obtained with ISS in previous experiments.

[0122] DSS was then withdrawn for the following two weeks but afterwardit was reintroduced for an additional week. In this group no detectableprotective effect for ISS on the second round of DSS-induced colitiswere observed (i.e., DAI>5). This finding suggest that long orprotracted treatment of gastrointestinal inflammation may requirecontinued immunomodulatory nucleic acid therapy in order to maintain thedesired therapeutic effect.

Example 6 Intragastric administration of ISS ameliorates symptoms in amouse model of colitis

[0123] Balb/c mice were treated with 30 μg/animal of ISS or M-ODN (asdescribed in Example 2) by intragastric administration. Two hours later,the animals were treated with DSS to induce colitis as described inExample 2 above. Naïve control animals (naïve) received neither DSS norpolynucleotide. Colitis control animals (DSS) received nopolynucleotide. Seven days after induction of colitis, mice were weighedand inspected for diarrhea and rectal bleeding. The mice weresacrificed, and the entire colon was dissected and its length measuredand weighed. Scores were defined as described in Example 2.

[0124] The results are shown in FIG. 5. This experiment shows that ISSexhibits a protective effect when administered intragastrically.

Example 7 Dose-Response of Intragastric ISS in an animal model ofulcerative colitis (DSS-induced)

[0125] ISS was administered to Balb/c mice intragastrically as describedin Example 1 above at varying doses (0 μg/animal, 10 μg/animal, 30μg/animal, and 100 μg/animal). Two hours later, DSS was administered byaddition to the drinking water ad libitum at a concentration of 2.5%.Seven days after induction of colitis, mice were weighed and inspectedfor diarrhea and rectal bleeding. The mice were sacrificed, and theentire colon was dissected and its length measured and weighed. Scoreswere again defined as described in Example 1. The results are providedin FIGS. 6A-6C.

Example 8 PCR Analysis of the Effect of ISS Upon Colonic Tissue fromDSS-Induced Inflammation

[0126] To evaluate the anti-inflammatory role of ISS on DSS-inducedcolitis, a single administration of ISS or M-ODN (10 μg/mouse;polynucleotides as described in Example 2) was delivered subcutaneously2 hrs prior to DSS challenge as described in Example 2. Mice weresacrificed 7 days later.

[0127] mRNAs were isolated from colonic and duodenal sections (5 mm persection) using Micro-FastTrack mRNA isolation kit [Invitrogen]. Afterisolation of mRNAs reverse transcriptase reactions were performed usingSuperScript™ First-strand synthesis system [GibcoBRL] according to amanufacture's protocol. Generated cDNAs were applied to PCR analysis forgene regulation of chemokines, cytokines and metalloproteinases. Thefollowing sets of oligonucleotides were used as primers for theindicated chemokines, cytokines, and metalloproteinases:

[0128] 1) IL-1β (sense) 5′-ATGAGCTTTGTACAAGGAGAACCA-3′ (SEQ ID NO:12)(anti-sense) 5′-TTAGGAAGACACAGATTCCATGGT-3′ (SEQ ID NO:13)

[0129] 2) IFN-γ (sense) 5′-GGTGACATGAAAATCCTGCAGAGC-3′ (SEQ ID NO:14)(antisense) 5′-TCAGCAGCGACTCCTTTTCCGCTT-3′ (SEQ ID NO:15)

[0130] 3) IL-12/p40 (sense) 5′-GGGACATCATCAAACCAGACC-3′ (SEQ ID NO:16)(anti-sense) 5′-GCCAACCAAGCAGAAGACAGC-3′ (SEQ ID NO:17)

[0131] 4) TGFβ(sense) 5′-GATACCAACTATTGCTTCAGCTCCACA-3′(SEQ ID NO: 18)(anti-sense) 5′-TCAGCTGCACTTGCAGGAGCGCACAAT-3′ (SEQ ID NO:19)

[0132] 5) TNFα(sense) 5′-ATCAGTTCTATGGCCCAGACCCTCACA-3 ′(SEQ ID NO:20)(anti-sense) 5 ′-TCACAGAGCAATGACTCCAAAGTAGAG-3 ′ (SEQ ID NO:21)

[0133] 6) MCP-2 (sense) 5′-ATGAAGATCTACGCAGTGCTTCTTTGC-3′(SEQ ID NO:22)(anti-sense)5′-TCAAGGCTGCAGAATTTGAGACTTCTG-3′ (SEQ ID NO:23)

[0134] 7) MCP-3 (sense) 5′-ATGAGGATCTCTGCCACGCTTCTGTGC-3′(SEQ ID NO:24)(anti-sense) 5′-AGGCTTTGGAGTTGGGGTTTTCATGTC-3′ (SEQ ID NO:25)

[0135] 8) MIP-2 (sense) 5′-ATGGCCCCTCCCACCTGCCGGCTCCTC-3′(SEQ ID NO:26)(anti-sense) 5′-AGGTACGATCCAGGCTTCCCGGGTGCT-3′ (SEQ ID NO:27)

[0136] 9) KC (sense) 5′-ATGATCCCAGCCACCCGCTCGCTTCTC-3′(SEQ ID NO:28)(anti-sense) 5′-TTACTTGGGGACACCTTTTAGCATCTT-3′ (SEQ ID NO:29)

[0137] 10) MMP-1 (sense) 5′-AACAAATACTGGAAGTTCAACAAC-3′(SEQ ID NO:30)(anti-sense) 5′-TCAGACCTTGTCCAGCAGCGAACG-3′ (SEQ ID NO:31)

[0138] 11) MMP-3 (sense) 5′-AAGGGGATCCCTGAATCACCTCAG-3′(SEQ ID NO:32)(anti-sense) 5′-TCACACCCACTCTTGCATAGACCG-3′ (SEQ ID NO:33)

[0139] 12) MMP-9 (sense)5′-TGGTACTGGAAGTTCCTGAATCATAGA-3′(SEQ ID NO:34)(anti-sense) 5′-CAAGGGCACTGCAGGAGGTCGTAGGTC-3′ (SEQ ID NO:35)

[0140] 13) MMP-10 (sense) 5′-GCAGTCCGAGGAAATGAAGTCCAA-3′(SEQ ID NO:36)(anti-sense) 5′-TCAGCACAGCAGCCAGCTGTTGCT-3′ (SEQ ID NO:37)

[0141] 14) G3PDH(sense) 5′-ACCACAGTCCATGCCATCAC-3′(SEQ ID NO:38)(anti-sense) 5′-TCCACCACCCTGTTGCTGTA-3′ (SEQ ID NO:39)

[0142] PCR was performed with 1 μl of RT mix, 20 pmol of each sense andanti-sense primer, 0.2 mM dNTPs, 2.5 mM MgC₂ and 2 units of Taq DNApolymerase to a final volume of 30 μl. The PCR cycling parameters were94° C. (30 sec), 68° C. (1 min) for 18 cycles and 24 cycles for G3PDHand for other test genes, respectively. PCR products were separated on1.5% agarose-gel and visualized by ethidium bromide staining.

[0143] Western blot analysis of MMP-10 levels was performed on colonictissues obtained from naive, DSS, DSS+M-ODN and DSS+ISS treated mice.Lysates (40 μg) were separated on 10-20 % Tricine SDS-PAGE, blotted onPVDF membrane and stained with rabbit anti-mouse MMP-10 or rabbitanti-mouse IL-1β antibodies (Chemicon, Tamecula Calif.).

[0144] Results are shown in FIGS. 7A-7F. Data shown represent one ofthree similar experiments with identical results. FIG. 7A shows that ISSinduces IL-12 and IFN-γ mRNA in colonic tissue of naïve animals. FIGS.7B-7D illustrate ISS inhibition of the induction of DSS-induced IL-1 andTNF-γ (FIG. 7B), the induction of chemokines such as; MCP-2, MIP-2 andKC (FIG. 7C), and the induction of matrix metalloproteinases such as;MMP-1, MMP-3, MMP-9 and MMP-10 (FIG. 7D). ISS also inhibited MMP-10induction, as shown by Western blot analysis (FIG. 7E). ISSadministration did not affect the expression of IL-1β, KC and MMP-10 inthe duodenum of DSS-treated mice (FIG. 7F).

Example 9 In Vivo Analysis of ISS Inhibition of DSS-Induced Inflammationand Cell Death

[0145] In order to evaluate whether ISS enhances mucosal restitution,the extent of colonic epithelial cell death in ISS treated mice wasevaluated both histologically and using the TUNEL assay. Mice weretreated with 10 μg /animal polynucleotide (ISS or control M-ODN as perExample 2) subcutaneously or with 30 μg/animal ISS, and DSS administeredtwo hours later as described in Example 2. Seven days after DSSadministration, the animals were sacrificed, and tissue sections (colon)were collected.

[0146] For histological analysis, the tissue sections were fixedovernight in 10% buffered formalin at room temperature and embedded inparaffin. The paraffin-embedded tissue section were further sectioned(5-μm thickness), stained with hematoxylin-eosin (H&E staining).Exemplary results are shown in FIGS. 8A-8D: FIG. 8A, control (no DSS, nopolynucleotide); FIG. 8B, DSS alone; FIG. 8C, DSS and subcutaneouscontrol M-ODN; FIG. 8D, DSS and subcutaneous ISS; and FIG. 8E, DSS andintragastric ISS.

[0147] In order to evaluate apoptosis of intestinal cells, apoptoticcells were detected in situ by the terminal deoxynucleotidyltransferase- mediated d-UTP nick end labeling (TUNEL) assay. Sampleswere labeled with in situ cell death detection kit (fluorescein; RocheMolecular Biochemical. Indianapolis, Ind.) according to themanufacture's instruction and observed under a fluorescent microscope(Olympus Optical Co., Lake Success, N.Y.). Three specimens from eachcolon were evaluated, and representative fields were photographed withan Olympus camera, equipped with a Sony DKC5000 charge-coupled device.The images were captured and processed for presentation with AdobePhotoshop 5.5 and printed on a dye sublimation printer. Exemplaryresults are shown in FIGS. 9A-9D: Figure, control (no DSS, nopolynucleotide); FIG. 9B, DSS alone; FIG. 9C, DSS and subcutaneouscontrol M-ODN; FIG. 9D, DSS and subcutaneous ISS; and FIG. 9E, DSS andintragastric ISS.

[0148] H&E staining demonstrated shortening of the epithelial crypts andthinning of epithelium, significant cellular infiltration in the laminapropria, and submucosal edema in the colon from DSS or M-ODN-treatedmice. Colonic architecture is preserved and cellular infiltration ismarkedly reduced in DSS+ISS treated mice. TUNEL assays were negative inISS treated mice and markedly positive in the control groups, asindicated by the multiple TUNEL positive cells at the colonic villoustip from DSS or from M-ODN-treated mice. These findings coincide withthe histological evaluation of colonic tissue that revealed normalmucosa and inflamed mucosa in ISS and control groups, respectively.

Example 10 In Vitro Analysis of ISS Inhibition of DSS-InducedInflammation and Cell Death

[0149] To further evaluate the effect of ISS on DSS-induced cell deathin vitro, bone marrow derived macrophages (BMDM) were cultured asdescribed (Martin-Orozco et al. Int Immunol (1999) 11:1111-8) for 7 daysand then incubated with 0.1% DSS in the presence or absence of ISS (1μg/ml) or control M-ODN (μg/ml). ISS or control M-ODN were added 2 hrsprior to treatment with DSS. BMDM cultured without DSS or ISS served asa control. Effects of ISS were also compared to caspase activity inducedby the apoptosis inhibitor ZVAD (50 mM).

[0150] Catalytic activity of the pro-apoptosis caspases, caspase 3 and9, was measured in cell lysates using fluorometric substrates, thecaspase-3-like Ac-DEVD-AMC and the caspase-9-like Ac-LEHD-AFC, asdescribed by Genini D et al., Blood (2000) 96:3537-43.

[0151] As shown in FIGS. 1OA and 10B, respectively, caspase 3 andcaspase 9 activities were significantly lower in the ISS treated groupin comparison to the DSS or to the DSS+M-ODN treated groups (p<0.05,Students' t test). Data shown represent one of three experiments withsimilar results. These data indicate that ISS protects cells fromapoptosis.

Example 11 ISS Ameliorates DNB-Induced Colitis

[0152] Colitis was induced in Balb/c mice by rectal instillation of2,4,6 -dinitrobenzene sulfonic acid (DNBS) at 1 mg/mouse, dissolved in0.1 ml of 50% ethanol. Treated animals received subcutaneous ISS orM-ODN (as described in Example 1; 10 μg/animal) two hrs prior toinduction of colitis or 48 hrs after induction of colitis. Mice weresacrificed seven days after DNBS administration. Disease activity indexand MPO activity were determined as in DSS induced colitis (see above).Data represent means ±SE. There are at least 6 mice per group. PanelsA-D represent one experiment out of two, which were performed. * denotesp<0.05 of ISS or M-ODN treated groups in comparison to the DNBS group(Students' t test for unpaired data, the non-parametric Mann Whitneytest and Chi Square test).

[0153] As shown in FIGS. 11A-11E, ISS treatment rescued mice fromDNBS-induced death (FIG. 11A). The disease activity index (DAI) (FIG.11B), change in body weight (FIG. 11C), colonic weight (FIG. 11D), andcolonic MPO activity (FIG. 11E) were also reduced in ISS treated animalsin comparison to mice in the other group which survived DNBS challenge.ISS administration 48 hrs after induction of colitis also resulted inreduced DAI (FIG. 11F).

Example 12 Effect of Immunomodulatory Nucleic Acid Upon Spontaneous IBDin an IL-10 Knockout Mouse (IL-10 KO)

[0154] Six week old IL-10 KO mice (Bhan et al. Immunol Rev (1999)169:195-207) were treated subcutaneously with M-ODN (50 μg/animal) orISS (50 μg/animal) every 7 days (ISS and M-ODN) or 14 days (ISS). Micewere followed for 4 weeks and the presence of disease reflected byrectal protrusion and bleeding was monitored, The results are shown inFIGS. 12A-12D. The dark portion of the bars represent the number ofanimals in the group presenting with disease, while the grey-shadedportion represents the percentage of animals that were healthy at theindicated timepoints.

Example 13 Effect of Genomic Bacterial DNA on DSS-Induced Colitis

[0155] Colitis was induced in mice by adding DSS 2.5% to the drinkingwater. Mice were treated 2 hours prior to the addition of DSS with 50μg/animal of lactobacillus (VSL) DNA, E. coli DNA, or calf thymus DNA(thymus). The DNA was isolated as whole genomic DNA from each of thesesources and was detoxified from LPS using methods well known in the art.

[0156] Mice were sacrificed after 7 days. Disease activity was measuredusing the disease activity index described above, a combined score ofdecrease in body weight and the presence of blood in the stool. Theresults are shown in FIGS. 13A-13B. The asterisk indicates significanceat the p<0.05 confidence level. These data demonstrate that genomicbacterial DNA can ameliorate colitis.

Example 14 ISS inhibits spontaneous release of inflammatory mediatorsfrom colonic mucosa of IBD patients

[0157] To evaluate whether the effects of ISS observed in the two modelsof experimental colitis are applicable to the human, colonic biopsieswere obtained from patients with active ulcerative colitis or Crohn'scolitis and organ cultured for 24 hours in the presence of ISS or M-ODN(10 μg of each) as previously described by Sharon P. et alGastroenterology (1978) 65; 638-40. The accumulation in the medium ofIFNγ and IL -1β were determined by ELISA (Biosource International,Camarillo, Calif.).

[0158] As shown in Table 2, ISS inhibit IL-1β and stimulate IFNγgeneration suggesting that the anti-inflammatory effects of ISS observedin mice are operating in the human. IFNγ and IL-β levels in ODN freemedia were 1.6±0.4 and 35.5±10 pg/mg of wet weight (mean±SE),respectively, and were considered as 100%. * denotes p<0.05 incomparison to IFNγ or IL-β generation obtained in ODN free media(Student's t test). TABLE 2 Effect of ISS-ODN on hIFNγ and hIL-βgeneration by colonic mucosa of IBD patients. Treatment Number ofpatients hIFNγ(%) hIL-1β(%) ISS-ODN 10 203 ± 37*  45 ± 7* M-ODN  7 103 ±14  119 ± 15

[0159] Those skilled in the art will appreciate that the conceptions andspecific embodiments disclosed in the foregoing description may bereadily utilized as a basis for modifying or designing other embodimentsfor carrying out the same purposes of the present invention.

1 39 1 22 DNA Artificial Sequence synthetic polynucleotide sequence 1tgactgtgaa cgttcgagat ga 22 2 22 DNA Artificial Sequence syntheticpolynucleotide sequence 2 tgactgtgtt ccttagagat ga 22 3 22 DNAArtificial Sequence synthetic polynucleotide sequence 3 tgactgtgaaccttagagat ga 22 4 22 DNA Artificial Sequence synthetic polynucleotidesequence 4 tgactgtgaa ggttcgagat ga 22 5 22 DNA Artificial Sequencesynthetic polynucleotide sequence 5 tgactgtgaa cgttagagat ga 22 6 22 DNAArtificial Sequence synthetic polynucleotide sequence 6 tgactgtgaacgttagagat ga 22 7 20 DNA Artificial Sequence synthetic polynucleotidesequence 7 tccatgacgt tcctgatgct 20 8 22 DNA Artificial Sequencesynthetic polynucleotide sequence 8 tgactgtgaa tgttagagat ga 22 9 22 DNAArtificial Sequence synthetic polynucleotide sequence 9 tgactgtggtcgttagagat ga 22 10 22 DNA Artificial Sequence synthetic polynucleotidesequence 10 tcgtcgtcgt cgtcgtcgtc gt 22 11 22 DNA Artificial Sequencesynthetic polynucleotide sequence 11 tgaaacgttc gcctgtcgtt ga 22 12 24DNA Artificial Sequence oligonucleotide primer 12 atgagctttg tacaaggagaacca 24 13 24 DNA Artificial Sequence oligonucleotide primer 13ttaggaagac acagattcca tggt 24 14 24 DNA Artificial Sequenceoligonucleotide primer 14 ggtgacatga aaatcctgca gagc 24 15 24 DNAArtificial Sequence oligonucleotide primer 15 tcagcagcga ctccttttcc gctt24 16 21 DNA Artificial Sequence oligonucleotide primer 16 gggacatcatcaaaccagac c 21 17 21 DNA Artificial Sequence oligonucleotide primer 17gccaaccaag cagaagacag c 21 18 27 DNA Artificial Sequence oligonucleotideprimer 18 gataccaact attgcttcag ctccaca 27 19 27 DNA Artificial Sequenceoligonucleotide primer 19 tcagctgcac ttgcaggagc gcacaat 27 20 27 DNAArtificial Sequence oligonucleotide primer 20 atcagttcta tggcccagaccctcaca 27 21 27 DNA Artificial Sequence oligonucleotide primer 21tcacagagca atgactccaa agtagag 27 22 27 DNA Artificial Sequenceoligonucleotide primer 22 atgaagatct acgcagtgct tctttgc 27 23 27 DNAArtificial Sequence oligonucleotide primer 23 tcaaggctgc agaatttgagacttctg 27 24 27 DNA Artificial Sequence oligonucleotide primer 24atgaggatct ctgccacgct tctgtgc 27 25 27 DNA Artificial Sequenceoligonucleotide primer 25 aggctttgga gttggggttt tcatgtc 27 26 27 DNAArtificial Sequence oligonucleotide primer 26 atggcccctc ccacctgccggctcctc 27 27 27 DNA Artificial Sequence oligonucleotide primer 27aggtacgatc caggcttccc gggtgct 27 28 27 DNA Artificial Sequenceoligonucleotide primer 28 atgatcccag ccacccgctc gcttctc 27 29 27 DNAArtificial Sequence oligonucleotide primer 29 ttacttgggg acaccttttagcatctt 27 30 24 DNA Artificial Sequence oligonucleotide primer 30aacaaatact ggaagttcaa caac 24 31 24 DNA Artificial Sequenceoligonucleotide primer 31 tcagaccttg tccagcagcg aacg 24 32 24 DNAArtificial Sequence oligonucleotide primer 32 aaggggatcc ctgaatcacc tcag24 33 24 DNA Artificial Sequence oligonucleotide primer 33 tcacacccactcttgcatag accg 24 34 27 DNA Artificial Sequence oligonucleotide primer34 tggtactgga agttcctgaa tcataga 27 35 27 DNA Artificial Sequenceoligonucleotide primer 35 caagggcact gcaggaggtc gtaggtc 27 36 24 DNAArtificial Sequence oligonucleotide primer 36 gcagtccgag gaaatgaagt ccaa24 37 24 DNA Artificial Sequence oligonucleotide primer 37 tcagcacagcagccagctgt tgct 24 38 20 DNA Artificial Sequence oligonucleotide primer38 accacagtcc atgccatcac 20 39 20 DNA Artificial Sequenceoligonucleotide primer 39 tccaccaccc tgttgctgta 20

What is claimed is:
 1. A method for ameliorating gastrointestinalinflammation in a subject comprising: administering to a subjectsuffering from gastrointestinal inflammation a formulation comprising animmunomodulatory nucleic acid to the subject, the immunomodulatorynucleic acid comprising the sequence 5′-CpG-3′, said administering beingin an amount effective to ameliorate a symptom of gastrointestinalinflammation in the subject; wherein gastrointestinal inflammation isameliorated in the subject.
 2. The method of claim 1, wherein theimmunomodulatory nucleic acid comprises the sequence5′-Purine-Purine-[C]-[G]-Pyrimidine-Pyrimidine-3′.
 3. The method ofclaim 1, wherein the immunomodulatory nucleic acid molecule comprises aCpG motif selected from the group consisting of: a)5′-Purine-TCG-Pyrimidine-Pyrimidine-3′; b) 5′-[TCG]_(n)-3′, where n isany integer that is 1 or greater; c)5′-Purine-Purine-CG-Pyrimidine-Pyrimidine-CG-3′; and d)5′-Purine-TCG-Pyrimidine-Pyrimidine-CG-3′
 4. The method of claim 1,wherein the immunomodulatory nucleic acid molecule is selected from thegroup consisting of an immunostimulatory oligodeoxyribonucleotide(ISS-ODN); an isolated bacterial genomic DNA. and plasmid DNA comprisingan immunomodulatory nucleic acid sequence.
 5. The method of claim 1,wherein the immunomodulatory nucleic acid molecule comprises a sequenceselected from the group consisting of: AACGCC, AACGCT, AACGTC, AACGTT,AGCGCC, AGCGCT, AGCGTC, AGCGTT, GACGCC, GACGCT, GACGTC, GACGTT, GGCGCC,GGCGCT, GGCGTC, GGCGTT, ATCGCC, ATCGCT, ATCGTC, ATCGTT, GTCGCC, GTCGCT,GTCGTC, GTCGTT, TCGTCG, TCGTCGTCG, AACGCCCG, AACGCTCG, AACGTCCG,AACGTTCG, AGCGCCCG, AGCGCTCG, AGCGTCCG, AGCGTTCG, GACGCCCG, GACGCTCG,GACGTCCG, GACGTTCG, GGCGCCCG, GGCGCTCG, GGCGTCCG, GGCGTTCG, ATCGCCCG,ATCGCTCG, ATCGTCCG, ATCGTTCG, GTCGCCCG, GTCGCTCG, GTCGTCCG, andGTCGTTCG.
 6. The method of claim 4, wherein the immunomodulatory nucleicacid molecule comprises at least one sequence selected from the groupconsisting of AACGTT, aacgttcg, aacgtt, gtcgtt, and tcgtcg.
 7. Themethod of claim 4, wherein the immunomodulatory nucleic acid moleculecomprises at least one sequence selected from the group consisting oftgactgtgaacgttcgagatga (SEQ ID NO: 1), tgactgtgaacgttagagatga (SEQ IDNO:5), tgactgtggtcgttagagatga (SEQ ID NO:9), tcgtcgtcgtcgtcgtcgtcgt (SEQID NO:10), and tgaaacgttcgcctgtcgttga (SEQ ID NO:11).
 8. The method ofclaim 1, wherein the immunomodulatory nucleic acid is administered via agastroenteral route.
 9. The method of claim 1, wherein the gastroenteralroute is oral, intranasal, intragastric or rectal
 10. The method ofclaim 1, wherein the immunomodulatory nucleic acid is administered by asystemic route.
 11. The method of claim 10, wherein the systemic routeis intradermal, intramuscular, subcutaneous or intravenous.
 12. Themethod of claim 1, wherein the immunomodulatory nucleic acid isadministered by a mucosal route.
 13. The method of claim 1, wherein thegastrointestinal inflammation is chronic gastrointestinal inflammation.14. The method of claim 13, wherein the chronic gastrointestinalinflammation is caused by inflammatory bowel disease.
 15. The method ofclaim 14, wherein the inflammatory bowel disease is ulcerative colitis.16. The method of claim 14, wherein the inflammatory bowel disease isCrohn's disease.
 17. The method of claim 14, wherein theimmunomodulatory nucleic acid is administered in conjunction with asteroid or an antibody directed against tumor necrosis factor-α (TNF-α).18. The method of claim 1, wherein the gastrointestinal inflammation isacute gastrointestinal inflammation.
 19. A method for amelioratinginflammatory bowel disease in a subject comprising: administering to asubject suffering from inflammatory bowel disease a formulationcomprising an immunomodulatory nucleic acid to the subject, theimmunomodulatory nucleic acid comprising the sequence5′-Purine-Purine-[C]-[G]-Pyrimidine-Pyrimidine-3′, said administeringbeing in an amount effective to ameliorate a symptom of inflammatorybowel disease in the subject; wherein inflammatory bowel disease isameliorated in the subject.
 20. The method of claim 19, wherein saidadministering is by an intragastric route.
 21. The method of claim 19,wherein said administering is by a subcutaneous route.
 22. A method forameliorating inflammatory bowel disease in a subject comprising:administering to a subject suffering from inflammatory bowel disease aformulation comprising an immunomodulatory nucleic acid to the subject,the immunomodulatory nucleic acid comprising at least one sequenceselected from the group consisting of tgactgtgaacgttcgagatga (SEQ ID NO:1), tgactgtgaacgttagagatga (SEQ ID NO:5), tgactgtggtcgttagagatga (SEQ IDNO:9), tcgtcgtcgtcgtcgtcgtcgt (SEQ ID NO: 10), andtgaaacgttcgcctgtcgttga (SEQ ID NO: 1), said administering being in anamount effective to ameliorate a symptom of inflammatory bowel diseasein the subject;
 23. A method for reducing inflammation caused by agastrointestinal inflammatory disease in a subject, the methodcomprising: administering to a subject suffering from gastrointestinalinflammatory disease a formulation comprising an immunomodulatorynucleic acid to the subject, the immunomodulatory nucleic acidcomprising the sequence 5′-CpG-3′, said administering being in an amounteffective to reduce inflammation caused by gastrointestinal inflammatorydisease in the subject; wherein inflammation caused by gastrointestinalinflammatory disease is reduced in the subject.
 24. The method of claim23, wherein the immunomodulatory nucleic acid comprises the sequence5′-Purine-Purine-[C]-[G]-Pyrimidine-Pyrimidine-3′.
 25. The method ofclaim 23, wherein the immunomodulatory nucleic acid molecule comprises aCpG motif selected from the group consisting of: a)5′-Purine-TCG-Pyrimidine-Pyrimidine-3′; b) 5′-[TCG]_(n)-3′, where n isany integer that is 1 or greater; c)5′-Purine-Purine-CG-Pyrimidine-Pyrimidine-CG-3′; and d)5′-Purine-TCG-Pyrimidine-Pyrimidine-CG-3′
 26. The method of claim 23,wherein the immunomodulatory nucleic acid molecule is selected from thegroup consisting of an immunostimulatory oligodeoxyribonucleotide(ISS-ODN); an isolated, detoxified bacterial polynucleotide; bacterialgenomic DNA; and a plasmid DNA comprising an immunomodulatory nucleicacid.
 27. The method of claim 23, wherein the immunomodulatory nucleicacid molecule comprises a sequence selected from the group consistingof: AACGCC, AACGCT, AACGTC, AACGTT, AGCGCC, AGCGCT, AGCGTC, AGCGTT,GACGCC, GACGCT, GACGTC, GACGTT, GGCGCC, GGCGCT, GGCGTC, GGCGTT, ATCGCC,ATCGCT, ATCGTC, ATCGTT, GTCGCC, GTCGCT, GTCGTC, GTCGTT, TCGTCG,TCGTCGTCG, AACGCCCG, AACGCTCG, AACGTCCG, AACGTTCG, AGCGCCCG, AGCGCTCG,AGCGTCCG, AGCGTTCG, GACGCCCG, GACGCTCG, GACGTCCG, GACGTTCG, GGCGCCCG,GGCGCTCG, GGCGTCCG, GGCGTTCG, ATCGCCCG, ATCGCTCG, ATCGTCCG, ATCGTTCG,GTCGCCCG, GTCGCTCG, GTCGTCCG, and GTCGTTCG.
 28. The method of claim 23,wherein the immunomodulatory nucleic acid molecule comprises thesequence at least one sequence selected from the group consisting ofaacgtt, aacgttcg, aacgtt, gtcgtt, and tcgtcg.
 29. The method of claim23, wherein the immunomodulatory nucleic acid comprises at least onesequence selected from the group consisting of tgactgtgaacgttcgagatga(SEQ ID NO: 1), tgactgtgaacgttagagatga (SEQ ID NO:5),tgactgtggtcgttagagatga (SEQ ID NO:9), tcgtcgtcgtcgtcgtcgtcgt (SEQ ID NO:10), and tgaaacgttcgcctgtcgttga (SEQ ID NO: 11).
 30. The method of claim23, wherein the immunomodulatory nucleic acid is administered via agastroenteral route.
 31. The method of claim 30, wherein thegastroenteral route is oral, intranasal, intragastric or rectal.
 32. Themethod of claim 23, wherein the immunomodulatory nucleic acid isadministered by a systemic route.
 33. The method of claim 32, whereinthe systemic route is intradermal, intramuscular, subcutaneous orintravenous.
 34. The method of claim 23 wherein the immunomodulatorynucleic acid is administered by a mucosal route.
 35. The method of claim23, wherein the gastrointestinal inflammation is chronicgastrointestinal inflammation.
 36. The method of claim 33, wherein thechronic gastrointestinal inflammation is caused by inflammatory boweldisease.
 37. The method of claim 36, wherein the immunomodulatorynucleic acid is administered in conjunction with a steroid or anantibody directed against tumor necrosis factor-α (TNF-α).
 38. Themethod of claim 35, wherein the chronic gastrointestinal inflammatorydisease is ulcerative colitis.
 39. The method of claim 35, wherein thechronic gastrointestinal inflammatory disease is Crohn's disease.
 40. Amethod for reducing inflammation caused by inflammatory bowel disease ina subject comprising: administering to a subject suffering frominflammatory bowel disease a formulation comprising an immunomodulatorynucleic acid to the subject, the immunomodulatory nucleic acidcomprising the sequence5′-Purine-Purine-[C]-[G]-Pyrimidine-Pyrimidine-3′, said administeringbeing in an amount effective to reduce inflammation caused byinflammatory bowel disease in the subject; wherein inflammation causedby inflammatory bowel disease is reduced in the subject.
 41. The methodof claim 40, wherein said administering is by an intragastric route. 42.The method of claim 40, wherein said administering is by a subcutaneousroute.
 43. The method of claim 40, wherein the inflammatory boweldisease is ulcerative colitis.
 44. The method of claim 40, whereinreduction of inflammation of ulcerative colitis further decreases therisk of colonic carcinoma.
 45. The method of claim 43, wherein theinflammatory bowel disease is Crohn's disease.
 46. A method for reducinginflammation of inflammatory bowel disease in a subject comprising:administering to a subject suffering from inflammatory bowel disease aformulation comprising an immunomodulatory nucleic acid to the subject,the immunomodulatory nucleic acid comprising at least one sequenceselected from the group consisting of tgactgtgaacgttcgagatga (SEQ IDNO:1), tgactgtgaacgttagagatga (SEQ ID NO:5), tgactgtggtcgttagagatga (SEQID NO:9), tcgtcgtcgtcgtcgtcgtcgt (SEQ ID NO: 10), andtgaaacgttcgcctgtcgttga (SEQ ID NO: 11), said administering being in anamount effective to reduce inflammation in the subject; whereininflammation caused by inflammatory bowel disease is reduced in thesubject.